Gas-phase hydrogen/deuterium exchange of positively charged mononucleotides by use of Fourier-transform ion cyclotron resonance mass spectrometry

The gas-phase structures of protonated (deoxy)nucleoside-5′- and 3′-monophosphates (mononucleotides) have been examined by the use of gas-phase hydrogen/deuterium (H/D) exchange and high-field Fourier-transform ion cyclotron resonance mass spectrometry. These nucleotides were reacted with three different deuterating reagents: ND 3, D 2O, and D 2S, of which ND 3 was the most effective. All mononucleotides fully exchanged their labile hydrogen for deuterium with ND 3 with the exception of deoxycytidine-3′-monophosphate, deoxyadenosine-5′-monophosphate, adenosine-5′-monophosphate, and adenosine-3′-monophosphate. Semiempirical calculations demonstrate the presence of hydrogen bonding upon protonation of the purine mononucleotides which may lead to incomplete H/D exchange. H/D exchange rates differed between the deoxymononucleotides and the ribomononucleotides, suggesting that the 2′-OH group plays an important role in the exchange process. Reactions of nucleosides and mononucleotides with D 2O demonstrate that a structure-specific long-lived ion–molecule complex between D 2O and the mononucleotide involving the phosphate group is necessary for exchange to overcome the high-energy activation barrier. In contrast, a structure-specific long-lived ion–molecule complex between the mononucleotides and ND 3 is not required for exchange to occur.